Multiple sequence alignment - TraesCS6D01G374900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6D01G374900 chr6D 100.000 2234 0 0 1 2234 458899856 458902089 0.000000e+00 4126
1 TraesCS6D01G374900 chr6D 98.569 2236 27 3 1 2234 124519196 124521428 0.000000e+00 3947
2 TraesCS6D01G374900 chr7D 98.791 2234 24 1 1 2234 382051753 382053983 0.000000e+00 3973
3 TraesCS6D01G374900 chr7D 98.612 2234 28 1 1 2234 381925675 381927905 0.000000e+00 3951
4 TraesCS6D01G374900 chr7D 98.482 2240 25 3 1 2234 381972096 381969860 0.000000e+00 3940
5 TraesCS6D01G374900 chr7D 98.255 2235 29 6 1 2234 203501673 203503898 0.000000e+00 3903
6 TraesCS6D01G374900 chr7D 96.774 62 1 1 2174 2234 626693989 626693928 3.920000e-18 102
7 TraesCS6D01G374900 chr1D 98.032 2236 37 4 1 2234 269408474 269410704 0.000000e+00 3879
8 TraesCS6D01G374900 chr7A 98.266 2192 29 3 1 2191 60280987 60283170 0.000000e+00 3829
9 TraesCS6D01G374900 chr7B 98.222 2193 29 4 1 2191 742991119 742993303 0.000000e+00 3825
10 TraesCS6D01G374900 chr7B 96.774 62 1 1 2174 2234 247490142 247490081 3.920000e-18 102
11 TraesCS6D01G374900 chr5A 98.174 2191 37 1 1 2191 238821134 238818947 0.000000e+00 3821
12 TraesCS6D01G374900 chr3A 98.361 61 1 0 2174 2234 227648530 227648590 8.440000e-20 108


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G374900 chr6D 458899856 458902089 2233 False 4126 4126 100.000 1 2234 1 chr6D.!!$F2 2233
1 TraesCS6D01G374900 chr6D 124519196 124521428 2232 False 3947 3947 98.569 1 2234 1 chr6D.!!$F1 2233
2 TraesCS6D01G374900 chr7D 382051753 382053983 2230 False 3973 3973 98.791 1 2234 1 chr7D.!!$F3 2233
3 TraesCS6D01G374900 chr7D 381925675 381927905 2230 False 3951 3951 98.612 1 2234 1 chr7D.!!$F2 2233
4 TraesCS6D01G374900 chr7D 381969860 381972096 2236 True 3940 3940 98.482 1 2234 1 chr7D.!!$R1 2233
5 TraesCS6D01G374900 chr7D 203501673 203503898 2225 False 3903 3903 98.255 1 2234 1 chr7D.!!$F1 2233
6 TraesCS6D01G374900 chr1D 269408474 269410704 2230 False 3879 3879 98.032 1 2234 1 chr1D.!!$F1 2233
7 TraesCS6D01G374900 chr7A 60280987 60283170 2183 False 3829 3829 98.266 1 2191 1 chr7A.!!$F1 2190
8 TraesCS6D01G374900 chr7B 742991119 742993303 2184 False 3825 3825 98.222 1 2191 1 chr7B.!!$F1 2190
9 TraesCS6D01G374900 chr5A 238818947 238821134 2187 True 3821 3821 98.174 1 2191 1 chr5A.!!$R1 2190

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
665 671 0.460987 CGAAGCACTGGAGTGATCCC 60.461 60.0 11.06 0.0 44.74 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1853 1874 1.376683 CGATGGGGAAACGGCAAGA 60.377 57.895 0.0 0.0 0.0 3.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
288 289 4.329462 TTTCCATTTTCGTTGGGAAAGG 57.671 40.909 0.00 0.0 44.95 3.11
665 671 0.460987 CGAAGCACTGGAGTGATCCC 60.461 60.000 11.06 0.0 44.74 3.85
888 904 3.304829 AGTAAGATCCTTGGCTCCTCTC 58.695 50.000 0.00 0.0 0.00 3.20
892 908 2.180973 AGATCCTTGGCTCCTCTCCATA 59.819 50.000 0.00 0.0 32.92 2.74
927 943 4.047125 CCCACATGGAAGCGGGGT 62.047 66.667 0.00 0.0 37.39 4.95
1012 1028 1.777272 AGAGGGGGATGGATAAAGTGC 59.223 52.381 0.00 0.0 0.00 4.40
1038 1054 7.464444 CGCAAAACAGACTCACATTTTTCAATT 60.464 33.333 0.00 0.0 0.00 2.32
1090 1109 9.236691 CGACAAAGAAAGAATCATCTTGAAAAA 57.763 29.630 2.77 0.0 45.19 1.94
1213 1233 1.679032 GGCAACTATCTCCTGCGGTTT 60.679 52.381 0.00 0.0 36.93 3.27
1536 1556 3.231818 AGGCTAAAAGCGAGATAGGCTA 58.768 45.455 13.45 0.0 46.81 3.93
1679 1700 3.038280 TGTCTGTCTCCTTTGTCCTTCA 58.962 45.455 0.00 0.0 0.00 3.02
1845 1866 1.202533 CCATCACGTGTCCAGATACCC 60.203 57.143 16.51 0.0 0.00 3.69
1853 1874 0.753262 GTCCAGATACCCGTGCATCT 59.247 55.000 0.00 0.0 31.58 2.90
1950 1971 2.345560 ACTTAGGTAAACAGGCACCCT 58.654 47.619 0.00 0.0 35.25 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.314357 CGTACAAGGATATGGAGTCGACA 59.686 47.826 19.50 0.00 0.00 4.35
288 289 2.552585 TTCGGATGGACTTCGCCGTC 62.553 60.000 0.00 0.00 43.92 4.79
353 354 3.126879 CCTTCCGCATGCGCTTCA 61.127 61.111 34.00 14.42 38.24 3.02
511 512 8.774546 TTAGATATCTGGATAGATGGATGGAC 57.225 38.462 15.79 0.00 43.41 4.02
888 904 3.226777 CAGAGACCCCTGTAGAGTATGG 58.773 54.545 0.00 0.00 0.00 2.74
892 908 0.324830 GGCAGAGACCCCTGTAGAGT 60.325 60.000 0.00 0.00 36.57 3.24
927 943 6.239317 CCCGTGTTTGATCTTATCCATCTCTA 60.239 42.308 0.00 0.00 0.00 2.43
1012 1028 4.797868 TGAAAAATGTGAGTCTGTTTTGCG 59.202 37.500 0.00 0.00 0.00 4.85
1038 1054 4.647399 ACGAAAAAGGAACCCATCTTTTCA 59.353 37.500 0.00 0.00 40.87 2.69
1090 1109 0.036671 CGAAGGGGTTAGGAGCGTTT 60.037 55.000 0.00 0.00 0.00 3.60
1091 1110 1.190178 ACGAAGGGGTTAGGAGCGTT 61.190 55.000 0.00 0.00 0.00 4.84
1092 1111 0.323725 TACGAAGGGGTTAGGAGCGT 60.324 55.000 0.00 0.00 0.00 5.07
1213 1233 2.225142 ACTAACAGCTGAGTCCTCTCCA 60.225 50.000 23.35 0.00 39.75 3.86
1536 1556 6.128007 CCTTTGTAAGCGAAAATGTCCAGTAT 60.128 38.462 0.00 0.00 0.00 2.12
1645 1665 6.402222 AGGAGACAGACAGAATTTACATCAC 58.598 40.000 0.00 0.00 0.00 3.06
1679 1700 4.333913 TCGGAGACTAGACTAGCGTTAT 57.666 45.455 9.52 0.00 0.00 1.89
1853 1874 1.376683 CGATGGGGAAACGGCAAGA 60.377 57.895 0.00 0.00 0.00 3.02
1987 2008 3.340928 GGTAGAAGTAATGGGCAAACGT 58.659 45.455 0.00 0.00 0.00 3.99


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.